def testFileCorruption(self):
"""
Test that corrupt mrcfiles are logged as expected.
"""
# Create a tmp dir for this test output
with tempfile.TemporaryDirectory() as tmpdir_name:
# Instantiate an Apple instance
apple_picker = Apple(output_dir=tmpdir_name)
# Get the path of an input mrcfile
with importlib_resources.path(
tests.saved_test_data, "sample.mrc"
) as good_mrc_path:
# Store bad mrc in tmp test dir so it gets cleaned up
bad_mrc_path = os.path.join(tmpdir_name, "bad.mrc")
# Copy mrc file
copyfile(good_mrc_path, bad_mrc_path)
# Open mrc file and soft corrupt it
with mrcfile.open(bad_mrc_path, "r+") as fh:
fh.header.map = -1
# Check that we get a WARNING
with self.assertLogs(level="WARNING") as logs:
_ = apple_picker.process_micrograph(bad_mrc_path, create_jpg=False)
# Check the message prefix
self.assertTrue(
"APPLE.picking mrcfile reporting 1 corruptions" in logs.output[0]
)
# Check the message contains the file path
self.assertTrue(bad_mrc_path in logs.output[0])
def apple(mrc_dir, mrc_file, output_dir, create_jpg):
"""Pick and save particles from one or more mrc files."""
# Exactly one of mrc_dir/mrc_file should be specified.
# We handle this manually here until Click supports mutually exclusive options.
if all([mrc_dir, mrc_file]) or not any([mrc_dir, mrc_file]):
raise UsageError('Specify one of --mrc_dir or --mrc_file.')
picker = Apple(output_dir)
if mrc_dir:
picker.process_folder(mrc_dir, create_jpg=create_jpg)
elif mrc_file:
picker.process_micrograph(mrc_file, create_jpg=create_jpg)
def testPickCenters(self):
# 440 particles with the following centers
centers = {
(1261, 149), (2635, 173), (1715, 167), ( 249, 183), ( 715, 189), (2535, 201), (1025, 209),
(1303, 215), (1453, 225), ( 555, 225), (1215, 241), (2165, 247), (3055, 237), ( 455, 257),
(2303, 261), ( 291, 315), (1647, 273), (3129, 283), (1815, 301), ( 165, 329), (2453, 307),
( 939, 331), (1319, 361), ( 875, 373), (3131, 353), (1955, 367), ( 389, 367), (1717, 367),
(1741, 375), (3211, 405), (3383, 401), (2879, 433), (1249, 451), ( 921, 493), (2649, 493),
(3091, 497), ( 783, 509), (2411, 507), (1507, 529), (3229, 539), ( 545, 619), (1997, 551),
(3317, 547), ( 747, 577), (1423, 613), (1645, 611), (2481, 615), ( 149, 621), (2969, 643),
(1795, 671), (1197, 653), ( 889, 671), (2081, 667), (2697, 665), ( 465, 685), (3387, 719),
(3113, 683), (3219, 709), (3109, 695), (3473, 705), ( 239, 733), ( 987, 709), (1687, 735),
(2223, 713), (1777, 719), (2051, 781), (2197, 733), ( 763, 727), ( 769, 725), (2337, 757),
( 153, 735), ( 403, 771), (1381, 811), (1207, 789), (3463, 821), (1691, 819), (2175, 819),
(3127, 849), (1169, 845), (1509, 847), (1905, 861), (1819, 865), (2937, 871), (3573, 861),
( 305, 883), (2273, 935), (1703, 885), (2397, 885), ( 959, 881), (2099, 963), (1989, 919),
(2473, 909), ( 159, 981), (1585, 929), ( 371, 953), (1139, 931), (1233, 941), (3199, 959),
(1163, 999), (1441, 985), (3581, 989), (3583, 993), (1905, 1029), (3681, 1029), ( 547, 1041),
(2621, 1065), (3171, 1071), (3035, 1089), (2117, 1079), (2897, 1081), (3433, 1067), (1019, 1075),
(1363, 1111), ( 355, 1117), (1463, 1137), ( 475, 1131), ( 485, 1129), (3241, 1139), (2725, 1181),
(2027, 1167), (3807, 1191), ( 873, 1199), (2547, 1275), (2793, 1237), (3695, 1231), (3267, 1237),
(1693, 1253), ( 347, 1255), (3121, 1267), (2957, 1267), ( 535, 1287), ( 157, 1299), (1905, 1303),
(1789, 1289), (1801, 1287), (2189, 1339), (2267, 1331), (1277, 1339), (3677, 1337), ( 255, 1369),
(1483, 1365), (3159, 1395), ( 945, 1397), (1739, 1393), (2647, 1427), (3837, 1421), (2461, 1439),
(3487, 1453), ( 485, 1459), (3085, 1461), (3209, 1455), ( 293, 1459), (3571, 1457), (3863, 1457),
(3219, 1459), (3225, 1459), (3729, 1467), (3899, 1489), (1443, 1491), (3469, 1497), (1473, 1555),
(1951, 1551), ( 991, 1535), (2281, 1541), (1649, 1545), (3807, 1547), (1685, 1557), ( 785, 1587),
(1689, 1559), ( 387, 1579), (1239, 1571), ( 417, 1569), (3031, 1607), (1115, 1607), (2699, 1629),
(3695, 1639), (3893, 1647), (1009, 1657), (1547, 1649), (1115, 1687), (1987, 1693), (3285, 1681),
(1333, 1689), (3581, 1727), ( 165, 1697), (1511, 1719), ( 325, 1717), (2703, 1735), ( 755, 1773),
(2765, 1729), (3363, 1757), ( 983, 1751), (3075, 1807), (2359, 1857), (1955, 1823), ( 859, 1839),
(3409, 1843), (3483, 1849), ( 939, 1849), ( 983, 1863), (2487, 1875), ( 357, 1885), (2825, 1903),
(2627, 1907), (1575, 1915), (1549, 1957), ( 255, 1923), ( 523, 1959), ( 857, 1947), (1911, 1939),
(1387, 1967), (3855, 1965), (1243, 1977), (2829, 2011), (2517, 1975), (1665, 2003), (3475, 1987),
( 883, 2015), ( 809, 2031), ( 547, 2055), (2655, 2043), (3611, 2047), (3289, 2097), (3185, 2113),
(3581, 2113), (1233, 2137), (3581, 2119), (3401, 2145), (3489, 2187), ( 223, 2181), (2439, 2177),
(1447, 2201), (2927, 2253), (2215, 2207), (2835, 2219), ( 289, 2219), (3657, 2237), (2245, 2259),
(1257, 2275), (3735, 2253), (2977, 2255), ( 817, 2327), (1811, 2281), (3367, 2281), (3539, 2295),
( 965, 2307), (2865, 2291), (3091, 2327), (2245, 2327), (1361, 2351), (3779, 2341), (3909, 2347),
(2707, 2367), (1017, 2365), (1965, 2395), (3363, 2387), (1245, 2381), (1663, 2361), ( 669, 2387),
(1529, 2387), (1653, 2407), (3921, 2415), ( 547, 2421), ( 437, 2427), (3577, 2457), (2243, 2467),
( 749, 2475), ( 317, 2475), (3419, 2479), (1765, 2507), (2143, 2487), (1111, 2497), (1225, 2521),
(3475, 2509), (1145, 2515), (3379, 2535), ( 691, 2533), (2935, 2543), (1367, 2553), (2415, 2563),
(2937, 2593), (2693, 2587), (3271, 2593), ( 393, 2591), (1887, 2593), ( 529, 2609), (3339, 2601),
( 255, 2601), (2601, 2595), ( 813, 2617), (1997, 2607), (2509, 2615), ( 699, 2625), (1777, 2631),
(3935, 2623), ( 895, 2643), (3907, 2641), (1865, 2645), ( 693, 2661), (1733, 2663), (1963, 2675),
(3251, 2703), (2381, 2683), (1733, 2679), (3439, 2685), ( 215, 2717), (2769, 2719), (1495, 2737),
(1083, 2735), (2153, 2743), (3577, 2741), (2683, 2751), (1087, 2765), (1741, 2757), (2789, 2779),
(1815, 2793), (1249, 2823), (1533, 2855), (1923, 2819), (2021, 2833), (2747, 2823), (1367, 2847),
(3523, 2825), (3321, 2831), (3529, 2851), (3651, 2847), (3075, 2871), ( 851, 2877), (1907, 2855),
(2359, 2871), ( 597, 2943), ( 533, 2889), ( 485, 2887), (3507, 2899), ( 959, 2901), (3523, 2905),
( 387, 2933), (3131, 2945), (3933, 2957), (1585, 2975), ( 841, 2983), (2179, 3037), ( 821, 3011),
(1251, 3039), (2559, 3045), (1943, 3053), (2297, 3053), (1371, 3055), (2469, 3051), ( 957, 3061),
(2777, 3061), (3877, 3063), ( 853, 3077), ( 719, 3071), ( 279, 3079), (3783, 3089), ( 439, 3095),
(1483, 3091), ( 531, 3149), ( 691, 3101), (2387, 3125), (1219, 3149), (2977, 3151), (2299, 3167),
(1737, 3193), (2037, 3283), ( 715, 3201), ( 993, 3197), (3901, 3227), (2163, 3247), ( 861, 3253),
( 499, 3301), (1345, 3311), ( 225, 3245), (1941, 3299), ( 747, 3299), (3221, 3295), (1495, 3309),
(1235, 3297), (3335, 3315), (2727, 3333), (1077, 3315), (2287, 3335), (3107, 3341), (1191, 3375),
(1705, 3403), ( 343, 3379), (3351, 3393), (1869, 3385), (3763, 3403), ( 827, 3401), (2769, 3405),
(1805, 3423), (3079, 3441), ( 925, 3509), (1187, 3457), (3367, 3463), ( 379, 3471), (3007, 3499),
(1917, 3529), (2501, 3491), ( 725, 3491), (2327, 3477), (3331, 3485), (2391, 3509), (1087, 3501),
(2701, 3553), (3593, 3533), (2011, 3561), ( 583, 3559), (2581, 3575), (2131, 3587), (1565, 3571),
(3435, 3577), (1579, 3577), (3763, 3583), (3943, 3579), (2403, 3619), ( 505, 3611), ( 697, 3609),
(1023, 3621), ( 355, 3623), (3593, 3653), ( 327, 3673), (3273, 3685), (2797, 3701), (1127, 3697),
(3819, 3711), (2657, 3719), (2829, 3753), (3059, 3739), (3159, 3763), ( 525, 3769), (2993, 3771),
(1169, 3799), (1507, 3785), (1733, 3781), (2655, 3847), (2053, 3861), (2855, 3883)
}
apple_picker = Apple()
with importlib_resources.path(tests.saved_test_data, 'sample.mrc') as mrc_path:
centers_found = apple_picker.process_micrograph(mrc_path)
for center_found in centers_found:
_x, _y = tuple(center_found)
if (_x, _y) not in centers:
self.fail('({}, {}) not an expected center.'.format(_x, _y))
else:
centers.remove((_x, _y))
if centers:
self.fail('Not all expected centers were found!')
import logging import matplotlib.pyplot as plt import mrcfile from aspire.apple.apple import Apple logger = logging.getLogger(__name__) # %% # Load Micrograph Data # -------------------- # # Initiate ASPIRE's ``Apple`` class and load the micrograph data. apple_picker = Apple() filename = "data/falcon_2012_06_12-14_33_35_0.mrc" # %% # Pick Particles and Find Centers # ------------------------------- # # Here we use the ``process_micrograph`` method from the ``Apple`` class to find particles in the micrograph. centers = apple_picker.process_micrograph(filename, show_progress=False) # %% # Read Micrograph # --------------- with mrcfile.open(filename, mode="r") as mrc: